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Frances H. Arnold, a California Institute of Technology researcher, has won the 2011 Draper Prize, often described as the Nobel Prize for engineering, for her pioneering work on “directed evolution.”

The technique, a way to use evolution to engineer biology, has broad application in the fields of alternative energy and medicine.

Arnold, a professor of chemical engineering, is the first woman to win the prize.

The 2011 Draper is also being awarded to Willem P.C. Stemmer, founder and CEO of Amunix Inc., a Mountain View, Calif., pharmaceutical firm. Amunix creates biopharmaceuticals that can be injected in monthly doses rather than daily doses, and improves on their delivery method--subcutaneous, rather than intravenous.

The prize was awarded for Arnold and Stemmer's “individual contributions to ‘directed evolution’…a milestone in biological research,” the academy said. The technique, it noted, “enables solutions in such areas as food ingredients, pharmaceuticals, toxicology, agricultural products, gene delivery systems, laundry aids and biofuels, among others.”

Biofuels research is a hot field, as scientists struggle to develop alternatives to oil. Many geologists believe that global oil production has peaked, and the U.S. is seeking to promote new fuels as a way to wean itself from imported oil. Oil combustion also emits carbon dioxide, a gas that traps heat in the atmosphere and contributes to climate change.

The $500,000 prize is to be presented in Washington on Feb. 22, two days after Arnold gives one of two plenary speeches to the annual meeting of the American Assn. for the Advancement of Science. “Her multi-disciplinary approach reveals insight into the way natural evolution might have occurred,” according to the AAAS.

The other plenary speech is to be given by John P. Holdren, President Obama’s science advisor.

Arnold, 54, said her Caltech laboratory develops designs to engineer complex biological systems as a way to show “why nature’s designs work the way they do. “ She added, “The code of life is like a Beethoven symphony. We have not yet learned how to write music like that. But evolution does it very well. I am learning how to use evolution to compose new music.”

The research draws on a variety of disciplines, including chemistry, molecular biology, chemical engineering and applied physics. “Enzymes are the catalysts of life--everything made by nature is made by enzymes,” Arnold said. “Microbes such as bacteria and yeast use enzymes to make fuels from biomass. We use directed evolution to perfect those enzymes and make new fuels efficiently.”

Directed evolution, she explained, can show that randomly mutating genes of a targeted protein, especially an enzyme, result in some new proteins having more desirable traits than they did before the mutation. By selecting the best proteins and repeating the process multiple times, Arnold and her students directed the evolution of the proteins until they had the desirable properties.

Arnold is listed as co-inventor on more than 30 U.S. patents and has served as science advisor to several companies, including Amyris, Codexis and Gevo Inc., a company she cofounded in 2005 to produce fuels from renewable resources. Shell, one of several oil companies funding alternative energy research, is using Codexis technology to develop advanced biofuels. Other potential markets include carbon capture, water treatment and chemicals.

In 2008, Arnold became one of eight living scientists to be elected to all three of the most prestigious scientific societies, the National Academy of Engineering, the Institute of Medicine and the National Academy of Sciences.

“Frances’ work has changed the way we think about biological engineering,” said David A. Tirrell, former chairman of Caltech’s Division of Chemistry and Chemical Engineering, at the time. “Her methods have been adopted by hundreds of laboratories around the world. It’s a beautiful example of a new idea that proved to be almost immediately applicable to a broad range of fundamental and practical problems.”

Stemmer, 59, has developed other technologies, including DNA shuffling, which became known as molecular breeding. He co-founded Maxygen, a company to commercialize the process. Stemmer has more than 90 U.S. patents.

The Draper Prize, founded in 1988, has been awarded to such scientists as Timothy Berners-Lee, who developed the World Wide Web; Ivan Getting and Bradford Parkinson who invented the Global Positioning System (GPS), and Frank Whittle and Hans von Ohain for developing the turbojet engine.